Are you using the correct ammo ( normal 40mm shells, not the 6-bound version for m32 )???
Both M79 and MZP-1 uses 40mm shells ( normal and incendiary ), the only deference is the sight of the M79 ( MZP doesn't have a sight ) and MZP have more fire rate and less recoil, but cost a bit more.

Anyways Flan's crafting is still bugged and if this is the problem, there is nothing I can do about.

Edit: Spawn the guns with NEI and see if they are working. If they work, my job is done.